Just wanted to update the progress I have been able to make on my own. I was able to fix the registry keys and eliminate the SHA256 errors. So I am only left with the 5 that fail the catalog check and the 2 that are missing. I am stuck at this point and any help you can provide would be appreciated.
Using the information on the website I tried to track down the packages that the original files are located in. The do not have a KB article numbers attached to them but are all linked (strangely enough) to two packages.
CBS_microsoft-windows-internetexplorer-optional-package and microsoft-windows-internetexplorer-vistaplus-update. I cannot find a package to download to try and recover these files.
Attached are the latest CBS and CSUR logs.